Whole-organ and whole-body 3D atlases enable cellome-wide profiling

Area of Science:

• Biotechnology
• Bioinformatics
• Microscopy

Background:

• Advancements in tissue clearing and light-sheet microscopy enable single-cell resolution analysis of whole organs and bodies.
• Comprehensive bioinformatics resources, such as digitized cellome maps, are currently limited.

Purpose of the Study:

• To present the CUBIC Organ/Body Atlas, a 3D single-cell-resolution reference for eleven adult mouse organs and a neonatal whole mouse body.
• To establish a common cellomics workflow for systems-level understanding of organisms.

Main Methods:

• Optimized tissue clearing protocols.
• Developed exMOVIE imaging system for organ-/body-wide 3D imaging with sufficient working distance and axial resolution.
• Enabled subsequent cell nuclei detection.

Main Results:

• Generated a 3D single-cell-resolution atlas for eleven adult mouse organs and a neonatal whole mouse body.
• The atlas facilitates comparative analysis among multiple samples at single-cell resolution.
• Demonstrated applications in organ development, disease state analysis, and whole-body immune cell profiling.

Conclusions:

• The CUBIC Organ/Body Atlas provides a valuable resource for systems biology.
• Contributes to establishing a common cellomics workflow.
• Advances understanding of physiological, developmental, and pathological processes.